Scribd
Upload
139 views3 pages

Quality Control Metrics in Whole Exome Sequencing

The document outlines key quality control metrics that are essential for ensuring the reliability of whole exome sequencing data. It discusses quality control measures for sample and library preparation quality, capture efficiency, sequencing metrics, variant calling accuracy, post-sequencing data checks, documentation of quality control procedures, and the importance of continuous monitoring and improvement of quality control. Robust quality control through regular assessment of metrics at each stage is vital for genomic studies and clinical applications using whole exome sequencing data.

Uploaded by

kwmopvru
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
139 views3 pages

Quality Control Metrics in Whole Exome Sequencing

The document outlines key quality control metrics that are essential for ensuring the reliability of whole exome sequencing data. It discusses quality control measures for sample and library preparation quality, capture efficiency, sequencing metrics, variant calling accuracy, post-sequencing data checks, documentation of quality control procedures, and the importance of continuous monitoring and improvement of quality control. Robust quality control through regular assessment of metrics at each stage is vital for genomic studies and clinical applications using whole exome sequencing data.

Uploaded by

kwmopvru
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 3

Quality Control Metrics in Whole Exome Sequencing

Introduction:

Whole Exome Sequencing (WES) is a powerful technique that allows the targeted sequencing
of all protein-coding regions of the genome. To ensure the reliability and accuracy of WES data,
comprehensive quality control (QC) measures are essential. This document outlines key QC
metrics for Whole Exome Sequencing.

Sample Quality Control:

a. DNA Integrity Assessment:

Agarose gel electrophoresis or Bioanalyzer profiles to assess DNA integrity.

b. Concentration Measurement:

Quantification of DNA concentration using fluorometric or spectrophotometric methods.

Library Preparation QC:

a. Library Size Distribution:

Assess the size distribution of libraries using Bioanalyzer or similar tools.

b. Library Concentration:

Quantify the concentration of libraries to ensure optimal input for sequencing.

Capture Efficiency:

a. On-Target Rate:

Measure the percentage of sequenced reads that align to the target regions.

b. Uniformity of Coverage:

Evaluate the evenness of sequence coverage across target regions.

Sequencing Metrics:

a. Read Quality:

Assess base quality scores to ensure high sequencing accuracy.

b. Sequencing Depth:

Evaluate the average depth of coverage to ensure sufficient data for variant calling.
c. Duplication Rate:

Monitor the rate of duplicate reads, which can affect variant calling accuracy.

d. Mapping Rate:

Calculate the percentage of reads that successfully align to the reference genome.

Variant Calling QC:

a. SNP and INDEL Accuracy:

Evaluate the accuracy of called variants using reference standards or orthogonal methods.

b. Transition/Transversion Ratio:

Examine the ratio of transitions to transversions in called variants.

c. False Positive Rate:

Assess the rate of false-positive variant calls through comparison with gold standards.

d. Genotype Concordance:

Compare genotypes with known references to ensure accuracy.

Post-Sequencing QC:

a. Data Integrity:

Check for any errors or anomalies in the raw sequencing data.

b. QC Metrics Summary:

Compile a summary report including key metrics for all QC stages.

Documentation and Reporting:

a. QC Pipeline Documentation:

Document the steps and parameters used in the QC pipeline.

b. QC Report:

Generate a comprehensive QC report for each sequenced sample, including all relevant
metrics.

Continuous Monitoring and Improvement:

a. Regular Monitoring:

Implement regular checks and monitoring of QC metrics during routine sequencing runs.
b. Feedback Loop:

Establish a feedback loop to address and improve any recurring QC issues.

Conclusion:

Robust quality control measures are essential for ensuring the accuracy and reliability of Whole
Exome Sequencing data. Regular monitoring and documentation of QC metrics contribute to
the overall success of genomic studies and clinical applications utilizing WES data.

Note: The specific tools, thresholds, and standards mentioned in this document may vary
depending on the sequencing platform and analysis pipeline used. It's essential to adapt QC
metrics based on the specific requirements and guidelines of the sequencing facility or project.

You might also like